diff --git a/CHANGES.rst b/CHANGES.rst
index 96b228613e78d8cc0140019a3b610455662af42b..eaf4adf3145189a50f3a3754a5ab4f1deefbe31a 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -9,6 +9,9 @@ Version 2.0.6
Release date to be decided.
+- Added `getGeneLocation` webservice method. Given a gene symbol and optional
+ genome build, it returns the location of the gene.
+
Version 2.0.5
-------------
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index bc9bf5a0780a382af267b3973b17b017c6a8ff77..18d934f7dbf6f3ba39fc06eaad9bc0320a67fb03 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -41,6 +41,23 @@ class SoapMessage(ComplexModel):
#SoapMessage
+class GeneLocation(ComplexModel):
+ """
+ Return type of SOAP method getGeneLocation.
+ """
+ __namespace__ = SOAP_NAMESPACE
+
+ gene = Mandatory.Unicode
+ start = Mandatory.Integer
+ stop = Mandatory.Integer
+ orientation = Mandatory.Unicode
+ chromosome_name = Mandatory.Unicode
+ chromosome_accession = Mandatory.Unicode
+ assembly_name = Mandatory.Unicode
+ assembly_alias = Mandatory.Unicode
+#GeneLocation
+
+
class Mapping(ComplexModel):
"""
Return type of SOAP method mappingInfo.
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index c65053587d4e3b7639df78bf6152100cbf39114a..27c3410ba7f969bb6cd4da7f77d2cc5841fa2d26 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -21,12 +21,13 @@ import os
import socket
from operator import attrgetter
from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.sql import func
import mutalyzer
from mutalyzer.config import settings
from mutalyzer.db import session
-from mutalyzer.db.models import (Assembly, BatchJob, BatchQueueItem,
- TranscriptMapping)
+from mutalyzer.db.models import (Assembly, Chromosome, BatchJob,
+ BatchQueueItem, TranscriptMapping)
from mutalyzer.output import Output
from mutalyzer.grammar import Grammar
from mutalyzer.sync import CacheSync
@@ -1296,6 +1297,87 @@ class MutalyzerService(ServiceBase):
return descriptions
#getdbSNPDescriptions
+
+ @srpc(Mandatory.Unicode, Unicode, _returns=GeneLocation)
+ def getGeneLocation(gene, build=None):
+ """
+ Get the location of a gene on the given genome build (assembly), using
+ the system's transcript mapping database.
+
+ @arg gene: Gene symbol.
+ @type gene: string
+ @arg build: Genome build (assembly) by name or alias. If omited,
+ the system's default assembly is used.
+ @type build: string
+
+ @return: Object with the following fields:
+ - gene: Gene symbol.
+ - start: Gene start position. If multiple transcripts for the gene
+ are known, this contains the lowest start position.
+ - stop: Gene stop position. If multiple transcripts for the gene are
+ known, this contains the highest stop position.
+ - orientation: Gene orientation, either 'forward' or 'reverse'.
+ - chromosome_name: Gene chromosome by name (e.g., 'chrX').
+ - chromosome_accession: Gene chromosome by accession (e.g.,
+ 'NC_000023.10').
+ - assembly_name: Selected genome build (assembly) by name (e.g.,
+ 'GRCh37').
+ - assembly_alias: Selected genome build (assembly) by alias (e.g.,
+ 'hg19').
+ """
+ output = Output(__file__)
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received request getGeneLocation(%s, %s)'
+ % (gene, build))
+
+ try:
+ assembly = Assembly.by_name_or_alias(build or
+ settings.DEFAULT_ASSEMBLY)
+ except NoResultFound:
+ output.addMessage(__file__, 4, "EARG", "EARG %s" % build)
+ raise Fault("EARG",
+ "The build argument (%s) was not a valid " \
+ "build name." % build)
+
+ # From all the transcripts for this gene, get the lowest start
+ # position and highest stop position. For integrity, we group by
+ # chromosome and orientation.
+ mapping = \
+ session.query(func.min(TranscriptMapping.start),
+ func.max(TranscriptMapping.stop),
+ TranscriptMapping.orientation,
+ Chromosome) \
+ .filter(TranscriptMapping.chromosome.has(assembly=assembly),
+ TranscriptMapping.gene == gene) \
+ .join(TranscriptMapping.chromosome) \
+ .group_by(TranscriptMapping.chromosome,
+ TranscriptMapping.orientation) \
+ .first()
+
+ if not mapping:
+ output.addMessage(__file__, 4, "EARG", "EARG %s" % gene)
+ raise Fault("EARG",
+ "No location was found for gene %s." % gene)
+
+ start, stop, orientation, chromosome = mapping
+
+ result = GeneLocation()
+ result.gene = gene
+ result.start = start
+ result.stop = stop
+ result.orientation = orientation
+ result.chromosome_name = chromosome.name
+ result.chromosome_accession = chromosome.accession
+ result.assembly_name = assembly.name
+ result.assembly_alias = assembly.alias
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished processing getGeneLocation(%s %s)'
+ % (gene, build))
+
+ return result
+ #getGeneLocation
#MutalyzerService
diff --git a/tests/test_services_json.py b/tests/test_services_json.py
index 81833505e36ecee7436bde0f956e579ecd82c00e..5ca81daef7b476993167fec26e1e7d47da2dbb81 100644
--- a/tests/test_services_json.py
+++ b/tests/test_services_json.py
@@ -5,8 +5,11 @@ Tests for the JSON interface to Mutalyzer.
from __future__ import unicode_literals
+import pytest
import simplejson as json
+from spyne.model.fault import Fault
from spyne.server.null import NullServer
+
import mutalyzer
from mutalyzer import announce
from mutalyzer import Scheduler
@@ -142,3 +145,59 @@ class TestServicesJson(MutalyzerTest):
result = self._call('getBatchJob', job_id)
result = result.decode('base64').decode('utf-8').strip().split('\n')[1:]
assert expected == [line.split('\t') for line in result]
+
+ @fix(database, hg19, hg19_transcript_mappings)
+ def test_gene_location(self):
+ """
+ Get outer coordinates for gene.
+ """
+ r = self._call('getGeneLocation', 'SDHD', 'hg19')
+
+ assert r == {'gene': 'SDHD',
+ 'start': 111957571,
+ 'stop': 111966518,
+ 'orientation': 'forward',
+ 'chromosome_name': 'chr11',
+ 'chromosome_accession': 'NC_000011.9',
+ 'assembly_name': 'GRCh37',
+ 'assembly_alias': 'hg19'}
+
+ @fix(database, hg19, hg19_transcript_mappings)
+ def test_gene_location_reverse(self):
+ """
+ Get outer coordinates for gene on the reverse strand.
+ """
+ r = self._call('getGeneLocation', 'DMD', 'hg19')
+
+ assert r == {'gene': 'DMD',
+ 'start': 31137345,
+ 'stop': 33038317,
+ 'orientation': 'reverse',
+ 'chromosome_name': 'chrX',
+ 'chromosome_accession': 'NC_000023.10',
+ 'assembly_name': 'GRCh37',
+ 'assembly_alias': 'hg19'}
+
+ @fix(database, hg19, hg19_transcript_mappings)
+ def test_gene_location_default_build(self):
+ """
+ Get outer coordinates for gene without specifying the build.
+ """
+ r = self._call('getGeneLocation', 'SDHD')
+
+ assert r == {'gene': 'SDHD',
+ 'start': 111957571,
+ 'stop': 111966518,
+ 'orientation': 'forward',
+ 'chromosome_name': 'chr11',
+ 'chromosome_accession': 'NC_000011.9',
+ 'assembly_name': 'GRCh37',
+ 'assembly_alias': 'hg19'}
+
+ @fix(database, hg19, hg19_transcript_mappings)
+ def test_gene_location_invalid_gene(self):
+ """
+ Get outer coordinates for gene that does not exist.
+ """
+ with pytest.raises(Fault):
+ r = self._call('getGeneLocation', 'THISISNOTAGENE', 'hg19')